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Reverting bad exact model changes

This commit is contained in:
Mark DePristo 2011-11-21 16:14:40 -05:00
parent 1561af22af
commit ab2efe3bd3
1 changed files with 54 additions and 43 deletions
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21
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -339,7 +339,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
} }
final GenotypesContext calls = GenotypesContext.create(); GenotypesContext calls = GenotypesContext.create();
int startIdx = AFofMaxLikelihood; int startIdx = AFofMaxLikelihood;
for (int k = sampleIdx; k > 0; k--) { for (int k = sampleIdx; k > 0; k--) {
int bestGTguess; int bestGTguess;
@ -353,7 +354,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
double[] likelihoods = g.getLikelihoods().getAsVector(); double[] likelihoods = g.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL) {
if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) { if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) {
bestGTguess = Utils.findIndexOfMaxEntry(likelihoods); bestGTguess = Utils.findIndexOfMaxEntry(likelihoods);
} }
@ -391,11 +391,22 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods); final double qual = GenotypeLikelihoods.getQualFromLikelihoods(bestGTguess, likelihoods);
//System.out.println(myAlleles.toString());
calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false)); calls.add(new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
} else {
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(sample, NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
} }
for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
if ( !genotype.hasLikelihoods() )
continue;
Genotype g = GLs.get(genotype.getSampleName());
double[] likelihoods = genotype.getLikelihoods().getAsVector();
if (MathUtils.sum(likelihoods) <= SUM_GL_THRESH_NOCALL)
continue; // regular likelihoods
final double qual = Genotype.NO_LOG10_PERROR;
calls.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, qual, null, g.getAttributes(), false));
} }
return calls; return calls;